[2024-01-24 11:20:04,285] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:20:04,286] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:20:04,286] [INFO] DQC Reference Directory: /var/lib/cwl/stg0813c2aa-3884-4a5f-a2ab-c05493f87893/dqc_reference
[2024-01-24 11:20:05,419] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:20:05,420] [INFO] Task started: Prodigal
[2024-01-24 11:20:05,420] [INFO] Running command: gunzip -c /var/lib/cwl/stgc3953203-d6b1-499f-91ab-3d98c566facd/GCF_018316795.1_ASM1831679v1_genomic.fna.gz | prodigal -d GCF_018316795.1_ASM1831679v1_genomic.fna/cds.fna -a GCF_018316795.1_ASM1831679v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:25,369] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:25,370] [INFO] Task started: HMMsearch
[2024-01-24 11:20:25,370] [INFO] Running command: hmmsearch --tblout GCF_018316795.1_ASM1831679v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0813c2aa-3884-4a5f-a2ab-c05493f87893/dqc_reference/reference_markers.hmm GCF_018316795.1_ASM1831679v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:25,624] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:25,625] [INFO] Found 6/6 markers.
[2024-01-24 11:20:25,670] [INFO] Query marker FASTA was written to GCF_018316795.1_ASM1831679v1_genomic.fna/markers.fasta
[2024-01-24 11:20:25,671] [INFO] Task started: Blastn
[2024-01-24 11:20:25,671] [INFO] Running command: blastn -query GCF_018316795.1_ASM1831679v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0813c2aa-3884-4a5f-a2ab-c05493f87893/dqc_reference/reference_markers.fasta -out GCF_018316795.1_ASM1831679v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:26,920] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:26,923] [INFO] Selected 17 target genomes.
[2024-01-24 11:20:26,923] [INFO] Target genome list was writen to GCF_018316795.1_ASM1831679v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:26,929] [INFO] Task started: fastANI
[2024-01-24 11:20:26,929] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3953203-d6b1-499f-91ab-3d98c566facd/GCF_018316795.1_ASM1831679v1_genomic.fna.gz --refList GCF_018316795.1_ASM1831679v1_genomic.fna/target_genomes.txt --output GCF_018316795.1_ASM1831679v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:52,324] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:52,324] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0813c2aa-3884-4a5f-a2ab-c05493f87893/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:52,325] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0813c2aa-3884-4a5f-a2ab-c05493f87893/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:52,338] [INFO] Found 17 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 11:20:52,338] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:20:52,338] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Nocardiopsis dassonvillei subsp. dassonvillei	strain=DSM 43111	GCA_000092985.1	568208	2014	type	True	95.6264	1893	2200	95	conclusive
Nocardiopsis dassonvillei	strain=NCTC10488	GCA_900638215.1	2014	2014	type	True	95.6193	1900	2200	95	conclusive
Nocardiopsis dassonvillei	strain=ATCC 23218	GCA_012396345.1	2014	2014	type	True	95.5534	1781	2200	95	conclusive
Nocardiopsis dassonvillei subsp. crassaminis	strain=D1	GCA_902825375.1	2580523	2014	type	True	95.3439	1554	2200	95	conclusive
Nocardiopsis alborubida	strain=ATCC 23612	GCA_012396365.1	146802	146802	type	True	94.027	1835	2200	95	below_threshold
Nocardiopsis alborubida	strain=NBRC 13392	GCA_001552695.1	146802	146802	type	True	93.9894	1779	2200	95	below_threshold
Nocardiopsis deserti	strain=H13	GCA_008638355.1	2605988	2605988	type	True	93.9063	1865	2200	95	below_threshold
Nocardiopsis sinuspersici	strain=UTMC 00102	GCA_001998325.1	501010	501010	type	True	88.1719	1548	2200	95	below_threshold
Nocardiopsis aegyptia	strain=DSM 44442	GCA_013410755.1	220378	220378	type	True	83.7892	1423	2200	95	below_threshold
Nocardiopsis ganjiahuensis	strain=DSM 45031	GCA_000341085.1	239984	239984	type	True	83.6304	1405	2200	95	below_threshold
Nocardiopsis exhalans	strain=JCM11759T	GCA_024134545.1	163604	163604	type	True	83.6251	1326	2200	95	below_threshold
Nocardiopsis metallicus	strain=DSM 44598	GCA_014201115.1	179819	179819	type	True	83.5229	1365	2200	95	below_threshold
Nocardiopsis listeri	strain=NBRC 13360	GCA_001570765.1	53440	53440	type	True	82.6671	1182	2200	95	below_threshold
Nocardiopsis alkaliphila	strain=YIM 80379	GCA_000341005.1	225762	225762	type	True	82.1241	999	2200	95	below_threshold
Nocardiopsis kunsanensis	strain=DSM 44524	GCA_000340965.1	141693	141693	type	True	81.6664	1049	2200	95	below_threshold
Thermobifida alba	strain=DSM 43795	GCA_023208015.1	53522	53522	type	True	79.8487	810	2200	95	below_threshold
Streptomonospora litoralis	strain=M2	GCA_004323735.1	2498135	2498135	type	True	79.7633	883	2200	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:52,340] [INFO] DFAST Taxonomy check result was written to GCF_018316795.1_ASM1831679v1_genomic.fna/tc_result.tsv
[2024-01-24 11:20:52,340] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:52,340] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:52,341] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0813c2aa-3884-4a5f-a2ab-c05493f87893/dqc_reference/checkm_data
[2024-01-24 11:20:52,341] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:52,399] [INFO] Task started: CheckM
[2024-01-24 11:20:52,399] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018316795.1_ASM1831679v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018316795.1_ASM1831679v1_genomic.fna/checkm_input GCF_018316795.1_ASM1831679v1_genomic.fna/checkm_result
[2024-01-24 11:22:10,361] [INFO] Task succeeded: CheckM
[2024-01-24 11:22:10,362] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:22:10,381] [INFO] ===== Completeness check finished =====
[2024-01-24 11:22:10,382] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:22:10,382] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018316795.1_ASM1831679v1_genomic.fna/markers.fasta)
[2024-01-24 11:22:10,382] [INFO] Task started: Blastn
[2024-01-24 11:22:10,383] [INFO] Running command: blastn -query GCF_018316795.1_ASM1831679v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0813c2aa-3884-4a5f-a2ab-c05493f87893/dqc_reference/reference_markers_gtdb.fasta -out GCF_018316795.1_ASM1831679v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:22:12,353] [INFO] Task succeeded: Blastn
[2024-01-24 11:22:12,356] [INFO] Selected 11 target genomes.
[2024-01-24 11:22:12,356] [INFO] Target genome list was writen to GCF_018316795.1_ASM1831679v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:22:12,364] [INFO] Task started: fastANI
[2024-01-24 11:22:12,364] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3953203-d6b1-499f-91ab-3d98c566facd/GCF_018316795.1_ASM1831679v1_genomic.fna.gz --refList GCF_018316795.1_ASM1831679v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018316795.1_ASM1831679v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:22:30,288] [INFO] Task succeeded: fastANI
[2024-01-24 11:22:30,297] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:22:30,298] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_000092985.1	s__Nocardiopsis dassonvillei	95.6153	1894	2200	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	97.80	95.11	0.93	0.87	11	conclusive
GCF_012396365.1	s__Nocardiopsis alborubida	94.027	1835	2200	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	96.95	95.06	0.88	0.80	4	-
GCA_002529455.1	s__Nocardiopsis fusca	92.7976	1753	2200	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341065.1	s__Nocardiopsis halotolerans	88.9793	1460	2200	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905145.1	s__Nocardiopsis sp001905145	88.4123	1531	2200	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008638415.1	s__Nocardiopsis sinuspersici	88.1317	1531	2200	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	99.63	98.89	0.96	0.91	4	-
GCF_009830945.1	s__Nocardiopsis sp009830945	87.3805	1468	2200	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	99.72	99.66	0.93	0.93	3	-
GCF_001279585.1	s__Nocardiopsis sp001279585	84.0838	1343	2200	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410755.1	s__Nocardiopsis aegyptia	83.8228	1419	2200	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201115.1	s__Nocardiopsis metallicus	83.5339	1363	2200	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018207095.1	s__Nocardiopsis sp018207095	82.9286	1221	2200	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:22:30,299] [INFO] GTDB search result was written to GCF_018316795.1_ASM1831679v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:22:30,299] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:22:30,303] [INFO] DFAST_QC result json was written to GCF_018316795.1_ASM1831679v1_genomic.fna/dqc_result.json
[2024-01-24 11:22:30,303] [INFO] DFAST_QC completed!
[2024-01-24 11:22:30,303] [INFO] Total running time: 0h2m26s